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Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.

Porter NJ, Osko JD, Diedrich D, Kurz T, Hooker JM, Hansen FK, Christianson DW
J Med Chem 61 8054-8060 (2018)
Related entries: 6dvl, 6dvn, 6dvo

Cited: 35 times
EuropePMC logo PMID: 30118224

Abstract

Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop. Capping group interactions may also influence hydroxamate-Zn2+ coordination with monodentate or bidentate geometry.

Reviews - 6dvm mentioned but not cited (1)

  1. Structural determinants of affinity and selectivity in the binding of inhibitors to histone deacetylase 6. Osko JD, Christianson DW. Bioorg Med Chem Lett 30 127023 (2020)

Articles - 6dvm mentioned but not cited (2)

  1. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. Porter NJ, Osko JD, Diedrich D, Kurz T, Hooker JM, Hansen FK, Christianson DW. J Med Chem 61 8054-8060 (2018)
  2. Methods for the expression, purification, and crystallization of histone deacetylase 6-inhibitor complexes. Osko JD, Christianson DW. Methods Enzymol 626 447-474 (2019)


Reviews citing this publication (6)

  1. Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases. Porter NJ, Christianson DW. Curr Opin Struct Biol 59 9-18 (2019)
  2. Next-generation of selective histone deacetylase inhibitors. Yang F, Zhao N, Ge D, Chen Y. RSC Adv 9 19571-19583 (2019)
  3. A patent review of histone deacetylase 6 inhibitors in neurodegenerative diseases (2014-2019). Shen S, Kozikowski AP. Expert Opin Ther Pat 30 121-136 (2020)
  4. Bifunctional HDAC Therapeutics: One Drug to Rule Them All? Smalley JP, Cowley SM, Hodgkinson JT. Molecules 25 E4394 (2020)
  5. HDAC6 as a potential therapeutic target for peripheral nerve disorders. Prior R, Van Helleputte L, Klingl YE, Van Den Bosch L. Expert Opin Ther Targets 22 993-1007 (2018)
  6. HDAC6-an Emerging Target Against Chronic Myeloid Leukemia? Losson H, Schnekenburger M, Dicato M, Diederich M. Cancers (Basel) 12 E318 (2020)

Articles citing this publication (26)

  1. Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. Bhatia S, Krieger V, Groll M, Osko JD, Reßing N, Ahlert H, Borkhardt A, Kurz T, Christianson DW, Hauer J, Hansen FK. J Med Chem 61 10299-10309 (2018)
  2. Structural and in Vivo Characterization of Tubastatin A, a Widely Used Histone Deacetylase 6 Inhibitor. Shen S, Svoboda M, Zhang G, Cavasin MA, Motlova L, McKinsey TA, Eubanks JH, Bařinka C, Kozikowski AP. ACS Med Chem Lett 11 706-712 (2020)
  3. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Osko JD, Christianson DW. Biochemistry 58 4912-4924 (2019)
  4. Structure-Activity and Structure-Toxicity Relationships of Peptoid-Based Histone Deacetylase Inhibitors with Dual-Stage Antiplasmodial Activity. Mackwitz MKW, Hesping E, Antonova-Koch Y, Diedrich D, Woldearegai TG, Skinner-Adams T, Clarke M, Schöler A, Limbach L, Kurz T, Winzeler EA, Held J, Andrews KT, Hansen FK. ChemMedChem 14 912-926 (2019)
  5. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. Osko JD, Porter NJ, Narayana Reddy PA, Xiao YC, Rokka J, Jung M, Hooker JM, Salvino JM, Christianson DW. J Med Chem 63 295-308 (2020)
  6. One-pot, multi-component synthesis and structure-activity relationships of peptoid-based histone deacetylase (HDAC) inhibitors targeting malaria parasites. Diedrich D, Stenzel K, Hesping E, Antonova-Koch Y, Gebru T, Duffy S, Fisher G, Schöler A, Meister S, Kurz T, Avery VM, Winzeler EA, Held J, Andrews KT, Hansen FK. Eur J Med Chem 158 801-813 (2018)
  7. Fluorinated Analogues of the Histone Deacetylase Inhibitor Vorinostat (Zolinza): Validation of a Chiral Hybrid Bioisostere, BITE. Erdeljac N, Bussmann K, Schöler A, Hansen FK, Gilmour R. ACS Med Chem Lett 10 1336-1340 (2019)
  8. Molecular Basis for the Selective Inhibition of Histone Deacetylase 6 by a Mercaptoacetamide Inhibitor. Porter NJ, Shen S, Barinka C, Kozikowski AP, Christianson DW. ACS Med Chem Lett 9 1301-1305 (2018)
  9. Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups. Reßing N, Sönnichsen M, Osko JD, Schöler A, Schliehe-Diecks J, Skerhut A, Borkhardt A, Hauer J, Kassack MU, Christianson DW, Bhatia S, Hansen FK. J Med Chem 63 10339-10351 (2020)
  10. Multitarget Anticancer Agents Based on Histone Deacetylase and Protein Kinase CK2 inhibitors. Martínez R, Geronimo BD, Pastor M, Zapico JM, Coderch C, Panchuk R, Skorokhyd N, Maslyk M, Ramos A, de Pascual-Teresa B. Molecules 25 E1497 (2020)
  11. Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors. Sandrone G, Cukier CD, Zrubek K, Marchini M, Vergani B, Caprini G, Fossati G, Steinkühler C, Stevenazzi A. ACS Med Chem Lett 12 1810-1817 (2021)
  12. Unique Molecular Interaction with the Histone Deacetylase 6 Catalytic Tunnel: Crystallographic and Biological Characterization of a Model Chemotype. Olaoye OO, Watson PR, Nawar N, Geletu M, Sedighi A, Bukhari S, Raouf YS, Manaswiyoungkul P, Erdogan F, Abdeldayem A, Cabral AD, Hassan MM, Toutah K, Shouksmith AE, Gawel JM, Israelian J, Radu TB, Kachhiyapatel N, de Araujo ED, Christianson DW, Gunning PT. J Med Chem 64 2691-2704 (2021)
  13. Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines. Nencetti S, Cuffaro D, Nuti E, Ciccone L, Rossello A, Fabbi M, Ballante F, Ortore G, Carbotti G, Campelli F, Banti I, Gangemi R, Marshall GR, Orlandini E. J Enzyme Inhib Med Chem 36 34-47 (2021)
  14. Spiroindoline-Capped Selective HDAC6 Inhibitors: Design, Synthesis, Structural Analysis, and Biological Evaluation. Saraswati AP, Relitti N, Brindisi M, Osko JD, Chemi G, Federico S, Grillo A, Brogi S, McCabe NH, Turkington RC, Ibrahim O, O'Sullivan J, Lamponi S, Ghanim M, Kelly VP, Zisterer D, Amet R, Hannon Barroeta P, Vanni F, Ulivieri C, Herp D, Sarno F, Di Costanzo A, Saccoccia F, Ruberti G, Jung M, Altucci L, Gemma S, Butini S, Christianson DW, Campiani G. ACS Med Chem Lett 11 2268-2276 (2020)
  15. Design, synthesis and biological evaluation of β-peptoid-capped HDAC inhibitors with anti-neuroblastoma and anti-glioblastoma activity. Reßing N, Marquardt V, Gertzen CGW, Schöler A, Schramm A, Kurz T, Gohlke H, Aigner A, Remke M, Hansen FK. Medchemcomm 10 1109-1115 (2019)
  16. Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia. Reßing N, Schliehe-Diecks J, Watson PR, Sönnichsen M, Cragin AD, Schöler A, Yang J, Schäker-Hübner L, Borkhardt A, Christianson DW, Bhatia S, Hansen FK. J Med Chem 65 15457-15472 (2022)
  17. First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement. Herp D, Ridinger J, Robaa D, Shinsky SA, Schmidtkunz K, Yesiloglu TZ, Bayer T, Steimbach RR, Herbst-Gervasoni CJ, Merz A, Romier C, Sehr P, Gunkel N, Miller AK, Christianson DW, Oehme I, Sippl W, Jung M. Chembiochem 23 e202200180 (2022)
  18. Inhibitors of histone deacetylase 6 based on a novel 3-hydroxy-isoxazole zinc binding group. Linciano P, Pinzi L, Belluti S, Chianese U, Benedetti R, Moi D, Altucci L, Franchini S, Imbriano C, Sorbi C, Rastelli G. J Enzyme Inhib Med Chem 36 2080-2086 (2021)
  19. In Vitro Assessment of the Genotoxic Hazard of Novel Hydroxamic Acid- and Benzamide-Type Histone Deacetylase Inhibitors (HDACi). Friedrich A, Assmann AS, Schumacher L, Stuijvenberg JV, Kassack MU, Schulz WA, Roos WP, Hansen FK, Pflieger M, Kurz T, Fritz G. Int J Mol Sci 21 E4747 (2020)
  20. Discovery of Histone Deacetylase Inhibitor Using Molecular Modeling and Free Energy Calculations. Mishra A, Singh A. ACS Omega 7 18786-18794 (2022)
  21. Discovery of novel benzohydroxamate-based histone deacetylase 6 (HDAC6) inhibitors with the ability to potentiate anti-PD-L1 immunotherapy in melanoma. Peng X, Yu Z, Surineni G, Deng B, Zhang M, Li C, Sun Z, Pan W, Liu Y, Liu S, Yu B, Chen J. J Enzyme Inhib Med Chem 38 2201408 (2023)
  22. Photocaged Histone Deacetylase Inhibitors as Prodrugs in Targeted Cancer Therapy. Kraft FB, Hanl M, Feller F, Schäker-Hübner L, Hansen FK. Pharmaceuticals (Basel) 16 356 (2023)
  23. The Effect of Vicinal Difluorination on the Conformation and Potency of Histone Deacetylase Inhibitors. Ariawan AD, Mansour F, Richardson N, Bhadbhade M, Ho J, Hunter L. Molecules 26 3974 (2021)
  24. Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6. Watson PR, Bai P, Wang C, Cragin AD, Hooker JM, Christianson DW. Biochemistry 61 1945-1954 (2022)
  25. Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6. Osko JD, Christianson DW. Acta Crystallogr F Struct Biol Commun 76 428-437 (2020)
  26. Crystal structure of histone deacetylase 6 complexed with (R)-lipoic acid, an essential cofactor in central carbon metabolism. Watson PR, Stollmaier JG, Christianson DW. J Biol Chem 299 105228 (2023)


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